Principles of MicroRNA–Target Recognition

TLDR

MicroRNAs are short non‑coding RNAs that regulate gene expression in plants and animals, yet the mechanisms by which they recognize and regulate target genes remain poorly understood. The study systematically evaluates the minimal requirements for functional miRNA–target duplexes in vivo and distinguishes target site classes with differing functional properties. The authors conducted systematic in vivo assays to determine minimal duplex requirements and classify target sites based on functional properties. They identified two broad target site classes—5′ dominant sites that function with strong 5′ pairing and minimal 3′ support, and 3′ compensatory sites that require strong 3′ pairing due to weak 5′ pairing—both used in biologically relevant genes, with an average miRNA targeting ~100 genes and miRNA 3′ ends being key determinants of specificity within families.

Abstract

MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression in plants and animals. Although their biological importance has become clear, how they recognize and regulate target genes remains less well understood. Here, we systematically evaluate the minimal requirements for functional miRNA–target duplexes in vivo and distinguish classes of target sites with different functional properties. Target sites can be grouped into two broad categories. 5′ dominant sites have sufficient complementarity to the miRNA 5′ end to function with little or no support from pairing to the miRNA 3′ end. Indeed, sites with 3′ pairing below the random noise level are functional given a strong 5′ end. In contrast, 3′ compensatory sites have insufficient 5′ pairing and require strong 3′ pairing for function. We present examples and genome-wide statistical support to show that both classes of sites are used in biologically relevant genes. We provide evidence that an average miRNA has approximately 100 target sites, indicating that miRNAs regulate a large fraction of protein-coding genes and that miRNA 3′ ends are key determinants of target specificity within miRNA families.